To start working with a git checkout:

1. Load the project in RStudio
2. Run roxygen2 over the package by selecting Build -> Document
3. Load the package with devtools::load_all()
4. Run data-raw/preprocess.R
5. Build -> Build and Reload

Summarized data files will be located in inst/extdata.

Column name	Description
FSC.A	Forward scatter AUC
FSC.H	Forward scatter peak height
FSC.W	Forward scatter peak width
SSC.*	Side scatter; as above
CD86	Scale value for CD86 staining intensity
CD206	Scale value for CD206 staining intensity
Time	Time to event from acquisition start (s)
Event..	Event serial number
Filename	Filename of original FCS file
Experiment	Replicate ID
antibody	"exp" (CD206/CD86) or "iso" (isotype controls)
m1_concentration	[LPS+IFN-γ] (ng/ml)
m2_concentration	[IL-4+IL-13] (ng/ml)
timepoint (if applicable)	Duration of incubation with cytokines (h)

See the vignettes for examples of normalizing data. Grouping on the antibody column is critical when plotting or summarizing data!